Transport through an electrostatically defined quantum dot lattice in a two-dimensional electron gas

Quantum dot lattices (QDLs) have the potential to allow for the tailoring of optical, magnetic, and electronic properties of a user-defined artificial solid. We use a dual gated device structure to controllably tune the potential landscape in a GaAs/AlGaAs two-dimensional electron gas, thereby enabling the formation of a periodic QDL. The current-voltage characteristics, I (V), follow a power law, as expected for a QDL. In addition, a systematic study of the scaling behavior of I (V) allows us to probe the effects of background disorder on transport through the QDL. Our results are particularly important for semiconductor-based QDL architectures which aim to probe collective phenomena.

RepEx: Repeat extractor for biological sequences

Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence (s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy. (C) 2013 Elsevier Inc. All rights reserved.

R-parameter: A local truncation error based adaptive framework for finite volume compressible flow solvers

A residual-based strategy to estimate the local truncation error in a finite volume framework for steady compressible flows is proposed. This estimator, referred to as the -parameter, is derived from the imbalance arising from the use of an exact operator on the numerical solution for conservation laws. The behaviour of the residual estimator for linear and non-linear hyperbolic problems is systematically analysed. The relationship of the residual to the global error is also studied. The -parameter is used to derive a target length scale and consequently devise a suitable criterion for refinement/derefinement. This strategy, devoid of any user-defined parameters, is validated using two standard test cases involving smooth flows. A hybrid adaptive strategy based on both the error indicators and the -parameter, for flows involving shocks is also developed. Numerical studies on several compressible flow cases show that the adaptive algorithm performs excellently well in both two and three dimensions.

Effects of mould filling on evolution of the solid-liquid interface during solidification

This work presents a numerical analysis of simultaneous mould filling and phase change for solidification in a two-dimensional rectangular cavity. The role of residual flow strength and temperature gradients within the solidifying domain, caused by the filling process, on the evolution of solidification interface are investigated. An implicit volume of fluid (VOF)-based algorithm has been employed for simulating the free surface flows during the filling process, while the model for solidification is based on a fixed-grid enthalpy-based control volume approach. Solidification modeling is coupled with VOF through User Defined Functions developed in the commercial computational fluid dynamics (CFD) code FLUENT 6.3.26. Comparison between results of the conventional analysis without filling effect and those of the present analysis shows that the residual flow resulting from the filling process significantly influences the progress of the solidification interface. A parametric study is also performed with variables such as cooling rate, filling velocity and filling configuration, in order to investigate the coupled effects of the buoyancy-driven flow and the residual flow on the solidification behavior.

SSMBS: a web server to locate sequentially separated motifs in biological sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server, SSMBS, which can locate anddisplay the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

A Method to Find Sequentially Separated Motifs in Biological Sequences (SSMBS)

Sequence motifs occurring in a particular order in proteins or DNA have been proved to be of biological interest. In this paper, a new method to locate the occurrences of up to five user-defined motifs in a specified order in large proteins and in nucleotide sequence databases is proposed. It has been designed using the concept of quantifiers in regular expressions and linked lists for data storage. The application of this method includes the extraction of relevant consensus regions from biological sequences. This might be useful in clustering of protein families as well as to study the correlation between positions of motifs and their functional sites in DNA sequences.

WebGeSTer DB-a transcription terminator database

We present WebGeSTer DB, the largest database of intrinsic transcription terminators (http://pallab.serc.iisc.ernet.in/gester). The database comprises of a million terminators identified in 1060 bacterial genome sequences and 798 plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined parameters. The results are arranged in different tiers to facilitate retrieval, as per the specific requirements. An interactive map has been incorporated to visualize the distribution of terminators across the whole genome. Analysis of the results, both at the whole-genome level and with respect to terminators downstream of specific genes, offers insight into the prevalence of canonical and non-canonical terminators across different phyla. The data in the database reinforce the paradigm that intrinsic termination is a conserved and efficient regulatory mechanism in bacteria. Our database is freely accessible.

Stabilized SPH-based simulations of impact dynamics using acceleration-corrected artificial viscosity

Artificial viscosity in SPH-based computations of impact dynamics is a numerical artifice that helps stabilize spurious oscillations near the shock fronts and requires certain user-defined parameters. Improper choice of these parameters may lead to spurious entropy generation within the discretized system and make it over-dissipative. This is of particular concern in impact mechanics problems wherein the transient structural response may depend sensitively on the transfer of momentum and kinetic energy due to impact. In order to address this difficulty, an acceleration correction algorithm was proposed in Shaw and Reid (''Heuristic acceleration correction algorithm for use in SPH computations in impact mechanics'', Comput. Methods Appl. Mech. Engrg., 198, 3962-3974) and further rationalized in Shaw et al. (An Optimally Corrected Form of Acceleration Correction Algorithm within SPH-based Simulations of Solid Mechanics, submitted to Comput. Methods Appl. Mech. Engrg). It was shown that the acceleration correction algorithm removes spurious high frequency oscillations in the computed response whilst retaining the stabilizing characteristics of the artificial viscosity in the presence of shocks and layers with sharp gradients. In this paper, we aim at gathering further insights into the acceleration correction algorithm by further exploring its application to problems related to impact dynamics. The numerical evidence in this work thus establishes that, together with the acceleration correction algorithm, SPH can be used as an accurate and efficient tool in dynamic, inelastic structural mechanics. (C) 2011 Elsevier Ltd. All rights reserved.

SuSeFLAV 1.2: Program for supersymmetric mass spectra with seesaw mechanism and rare lepton flavor violating decays

Accurate supersymmetric spectra are required to confront data from direct and indirect searches of supersymmetry. SuSeFLAV is a numerical tool capable of computing supersymmetric spectra precisely for various supersymmetric breaking scenarios applicable even in the presence of flavor violation. The program solves MSSM RGEs with complete 3 x 3 flavor mixing at 2-loop level and one loop finite threshold corrections to all MSSM parameters by incorporating radiative electroweak symmetry breaking conditions. The program also incorporates the Type-I seesaw mechanism with three massive right handed neutrinos at user defined mass scales and mixing. It also computes branching ratios of flavor violating processes such as l(j) -> l(i)gamma, l(j) -> 3 l(i), b -> s gamma and supersymmetric contributions to flavor conserving quantities such as (g(mu) - 2). A large choice of executables suitable for various operations of the program are provided. Program summary Program title: SuSeFLAV Catalogue identifier: AEOD_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEOD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 76552 No. of bytes in distributed program, including test data, etc.: 582787 Distribution format: tar.gz Programming language: Fortran 95. Computer: Personal Computer, Work-Station. Operating system: Linux, Unix. Classification: 11.6. Nature of problem: Determination of masses and mixing of supersymmetric particles within the context of MSSM with conserved R-parity with and without the presence of Type-I seesaw. Inter-generational mixing is considered while calculating the mass spectrum. Supersymmetry breaking parameters are taken as inputs at a high scale specified by the mechanism of supersymmetry breaking. RG equations including full inter-generational mixing are then used to evolve these parameters up to the electroweak breaking scale. The low energy supersymmetric spectrum is calculated at the scale where successful radiative electroweak symmetry breaking occurs. At weak scale standard model fermion masses, gauge couplings are determined including the supersymmetric radiative corrections. Once the spectrum is computed, the program proceeds to various lepton flavor violating observables (e.g., BR(mu -> e gamma), BR(tau -> mu gamma) etc.) at the weak scale. Solution method: Two loop RGEs with full 3 x 3 flavor mixing for all supersymmetry breaking parameters are used to compute the low energy supersymmetric mass spectrum. An adaptive step size Runge-Kutta method is used to solve the RGEs numerically between the high scale and the electroweak breaking scale. Iterative procedure is employed to get the consistent radiative electroweak symmetry breaking condition. The masses of the supersymmetric particles are computed at 1-loop order. The third generation SM particles and the gauge couplings are evaluated at the 1-loop order including supersymmetric corrections. A further iteration of the full program is employed such that the SM masses and couplings are consistent with the supersymmetric particle spectrum. Additional comments: Several executables are presented for the user. Running time: 0.2 s on a Intel(R) Core(TM) i5 CPU 650 with 3.20 GHz. (c) 2012 Elsevier B.V. All rights reserved.

Statistical significance of episodes with general partial orders

Frequent episode discovery is one of the methods used for temporal pattern discovery in sequential data. An episode is a partially ordered set of nodes with each node associated with an event type. For more than a decade, algorithms existed for episode discovery only when the associated partial order is total (serial episode) or trivial (parallel episode). Recently, the literature has seen algorithms for discovering episodes with general partial orders. In frequent pattern mining, the threshold beyond which a pattern is inferred to be interesting is typically user-defined and arbitrary. One way of addressing this issue in the pattern mining literature has been based on the framework of statistical hypothesis testing. This paper presents a method of assessing statistical significance of episode patterns with general partial orders. A method is proposed to calculate thresholds, on the non-overlapped frequency, beyond which an episode pattern would be inferred to be statistically significant. The method is first explained for the case of injective episodes with general partial orders. An injective episode is one where event-types are not allowed to repeat. Later it is pointed out how the method can be extended to the class of all episodes. The significance threshold calculations for general partial order episodes proposed here also generalize the existing significance results for serial episodes. Through simulations studies, the usefulness of these statistical thresholds in pruning uninteresting patterns is illustrated. (C) 2014 Elsevier Inc. All rights reserved.

THE BERGMAN KERNEL FUNCTION

In this note, we point out that a large family of n x n matrix valued kernel functions defined on the unit disc D subset of C, which were constructed recently in [9], behave like the familiar Bergman kernel function on ID in several different ways. We show that a number of questions involving the multiplication operator on the corresponding Hilbert space of holomorphic functions on D can be answered using this likeness.

A modified sulphide capacity function

The sulphide capacity as originally defined by Fincham and Richardson is a strong function of composition in pseudobinary oxide melts of interest in extractive metallurgy. From an analysis of data available in the literature, it is shown that sulphide capacity is directly proportional to the activity of the basic oxide in the melt, within the uncertainty of experimental data. A single parameter is sufficient to describe the sulphide capacity of a binary slag system under isothermal and isobaric conditions. The correlation indicates that the activity coefficient of the sulphide ion or the neutral base metal sulphide dissolved in the melt is independent of composition in pseudobinary melts within experimental uncertainty. Structural variations in the melt with composition do not seem to affect the activity coefficient of the sulphide. A modified sulphide capacity function is defined which makes the treatment more elegant and greatly simplifies data storage and retrieval. The modified function is not based on any model for the melt.

Pricing a Shared Access Link for Fair and Efficient Operation with Variable User Data Rates

The literature on pricing implicitly assumes an "infinite data" model, in which sources can sustain any data rate indefinitely. We assume a more realistic "finite data" model, in which sources occasionally run out of data; this leads to variable user data rates. Further, we assume that users have contracts with the service provider, specifying the rates at which they can inject traffic into the network. Our objective is to study how prices can be set such that a single link can be shared efficiently and fairly among users in a dynamically changing scenario where a subset of users occasionally has little data to send. User preferences are modelled by concave increasing utility functions. Further, we introduce two additional elements: a convex increasing disutility function and a convex increasing multiplicative congestion-penally function. The disutility function takes the shortfall (contracted rate minus present rate) as its argument, and essentially encourages users to send traffic at their contracted rates, while the congestion-penalty function discourages heavy users from sending excess data when the link is congested. We obtain simple necessary and sufficient conditions on prices for fair and efficient link sharing; moreover, we show that a single price for all users achieves this. We illustrate the ideas using a simple experiment.

Learning polyhedral classifiers using logistic function

In this paper we propose a new algorithm for learning polyhedral classifiers. In contrast to existing methods for learning polyhedral classifier which solve a constrained optimization problem, our method solves an unconstrained optimization problem. Our method is based on a logistic function based model for the posterior probability function. We propose an alternating optimization algorithm, namely, SPLA1 (Single Polyhedral Learning Algorithm1) which maximizes the loglikelihood of the training data to learn the parameters. We also extend our method to make it independent of any user specified parameter (e.g., number of hyperplanes required to form a polyhedral set) in SPLA2. We show the effectiveness of our approach with experiments on various synthetic and real world datasets and compare our approach with a standard decision tree method (OC1) and a constrained optimization based method for learning polyhedral sets.

Case for multiple views of function in design based on a common definition

Functions are important in designing. However, several issues hinder progress with the understanding and usage of functions: lack of a clear and overarching definition of function, lack of overall justifications for the inevitability of the multiple views of function, and scarcity of systematic attempts to relate these views with one another. To help resolve these, the objectives of this research are to propose a common definition of function that underlies the multiple views in literature and to identify and validate the views of function that are logically justified to be present in designing. Function is defined as a change intended by designers between two scenarios: before and after the introduction of the design. A framework is proposed that comprises the above definition of function and an empirically validated model of designing, extended generate, evaluate, modify, and select of state-change, and an action, part, phenomenon, input, organ, and effect model of causality (Known as GEMS of SAPPhIRE), comprising the views of activity, outcome, requirement-solution-information, and system-environment. The framework is used to identify the logically possible views of function in the context of designing and is validated by comparing these with the views of function in the literature. Describing the different views of function using the proposed framework should enable comparisons and determine relationships among the various views, leading to better understanding and usage of functions in designing.